test/jalview/fts/threedbeacons/TDBeaconsFTSRestClientTest.java

   1 package jalview.fts.threedbeacons;
   2
   3 import static org.testng.Assert.assertNull;
   4 import static org.testng.AssertJUnit.assertEquals;
   5 import static org.testng.AssertJUnit.assertTrue;
   6
   7 import java.net.URL;
   8 import java.nio.charset.StandardCharsets;
   9 import java.util.ArrayList;
  10 import java.util.Collection;
  11 import java.util.HashSet;
  12 import java.util.List;
  13 import java.util.Set;
  14
  15 import org.testng.Assert;
  16 import org.testng.annotations.AfterMethod;
  17 import org.testng.annotations.BeforeClass;
  18 import org.testng.annotations.BeforeMethod;
  19 import org.testng.annotations.Test;
  20
  21 import jalview.fts.api.FTSDataColumnI;
  22 import jalview.fts.api.FTSDataColumnI.FTSDataColumnGroupI;
  23 import jalview.fts.core.FTSRestClient;
  24 import jalview.fts.core.FTSRestRequest;
  25 import jalview.fts.core.FTSRestResponse;
  26 import jalview.fts.service.threedbeacons.TDBeaconsFTSRestClient;
  27 import jalview.gui.JvOptionPane;
  28
  29 public class TDBeaconsFTSRestClientTest
  30 {
  31   @BeforeClass(alwaysRun = true)
  32   public void setUpJvOptionPane()
  33   {
  34     JvOptionPane.setInteractiveMode(false);
  35     JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
  36   }
  37
  38   private FTSRestClient ftsRestClient;
  39
  40   @BeforeMethod(alwaysRun = true)
  41   public void setUp() throws Exception
  42   {
  43     ftsRestClient = new FTSRestClient()
  44     {
  45
  46       @Override
  47       public String getColumnDataConfigFileName()
  48       {
  49         return "/fts/tdbeacons_data_columns.txt";
  50       }
  51
  52       @Override
  53       public FTSRestResponse executeRequest(FTSRestRequest ftsRequest)
  54               throws Exception
  55       {
  56         return null;
  57       }
  58     };
  59   }
  60
  61   @AfterMethod(alwaysRun = true)
  62   public void tearDown() throws Exception
  63   {
  64   }
  65
  66   @Test
  67   public void getAllDefaulDisplayedDataColumns()
  68   {
  69     // to change when resources.tdbeacons_data_columns.txt is changed
  70     Assert.assertNotNull(
  71             ftsRestClient.getAllDefaultDisplayedFTSDataColumns());
  72     System.out
  73             .println(ftsRestClient.getAllDefaultDisplayedFTSDataColumns());
  74     Assert.assertTrue(!ftsRestClient.getAllDefaultDisplayedFTSDataColumns()
  75             .isEmpty());
  76     Assert.assertEquals(
  77             ftsRestClient.getAllDefaultDisplayedFTSDataColumns().size(),
  78             11);
  79   }
  80
  81   @Test(groups = { "Functional" })
  82   public void getPrimaryKeyColumIndexTest()
  83   {
  84     Collection<FTSDataColumnI> wantedFields = ftsRestClient
  85             .getAllDefaultDisplayedFTSDataColumns();
  86     int foundIndex = -1;
  87     try
  88     {
  89       Assert.assertEquals(foundIndex, -1);
  90       foundIndex = ftsRestClient.getPrimaryKeyColumIndex(wantedFields,
  91               false);
  92       Assert.assertEquals(foundIndex, 10);
  93       foundIndex = ftsRestClient.getPrimaryKeyColumIndex(wantedFields,
  94               true);
  95       Assert.assertEquals(foundIndex, 11);
  96     } catch (Exception e)
  97     {
  98       e.printStackTrace();
  99       Assert.fail("Exception thrown while testing...");
 100     }
 101   }
 102
 103   @Test(groups = { "Functional" })
 104   public void getDataColumnsFieldsAsCommaDelimitedString()
 105   {
 106     // to change when resources.tdbeacons_data_columns.txt is changed
 107     Collection<FTSDataColumnI> wantedFields = ftsRestClient
 108             .getAllDefaultDisplayedFTSDataColumns();
 109     String actual = ftsRestClient
 110             .getDataColumnsFieldsAsCommaDelimitedString(wantedFields);
 111     Assert.assertEquals(actual,
 112             "model_identifier,provider,model_category,uniprot_start,uniprot_end,resolution,qmean_avg_local_score,coverage,created,entry_name,model_url");
 113   }
 114
 115   @Test(groups = { "Functional" })
 116   public void getAllFTSDataColumns()
 117   {
 118     Collection<FTSDataColumnI> allFields = ftsRestClient
 119             .getAllFTSDataColumns();
 120     Assert.assertNotNull(allFields);
 121     // System.out.println(allFields.size());
 122     Assert.assertEquals(allFields.size(), 15);
 123   }
 124
 125   @Test(groups = { "Functional" })
 126   public void getSearchableDataColumns()
 127   {
 128     // to change when resources.tdbeacons_data_columns.txt is changed
 129     Collection<FTSDataColumnI> searchableFields = ftsRestClient
 130             .getSearchableDataColumns();
 131     Assert.assertNotNull(searchableFields);
 132     // System.out.println(searchableFields.size());
 133     Assert.assertEquals(searchableFields.size(), 1); // only 1: uniprot
 134                                                      // accession
 135   }
 136
 137   @Test(groups = { "Functional" })
 138   public void getPrimaryKeyColumn()
 139   {
 140     // to change when resources.tdbeacons_data_columns.txt is changed
 141     FTSDataColumnI expectedPKColumn;
 142     try
 143     {
 144       expectedPKColumn = ftsRestClient.getDataColumnByNameOrCode("Url");
 145       Assert.assertNotNull(ftsRestClient.getPrimaryKeyColumn());
 146       Assert.assertEquals(ftsRestClient.getPrimaryKeyColumn(),
 147               expectedPKColumn);
 148     } catch (Exception e)
 149     {
 150       e.printStackTrace();
 151       Assert.fail("Exception thrown while testing...");
 152     }
 153   }
 154
 155   @Test(groups = { "Functional" })
 156   public void getDataColumnByNameOrCode()
 157   {
 158     try
 159     {
 160       FTSDataColumnI foundDataCol = ftsRestClient
 161               .getDataColumnByNameOrCode("uniprot_accession");
 162       Assert.assertNotNull(foundDataCol);
 163       Assert.assertEquals(foundDataCol.getName(), "UniProt Accession");
 164     } catch (Exception e)
 165     {
 166       e.printStackTrace();
 167       Assert.fail("Exception thrown while testing...");
 168     }
 169   }
 170
 171   @Test(groups = { "Functional" })
 172   public void getDataColumnGroupById()
 173   {
 174     FTSDataColumnGroupI foundDataColGroup;
 175     try
 176     {
 177       foundDataColGroup = ftsRestClient.getDataColumnGroupById("g2");
 178       Assert.assertNotNull(foundDataColGroup);
 179       Assert.assertEquals(foundDataColGroup.getName(), "Quality");
 180     } catch (Exception e)
 181     {
 182       e.printStackTrace();
 183     }
 184   }
 185
 186   @Test(groups = { "Functional" })
 187   public void getDefaultResponsePageSize()
 188   {
 189     int defaultResSize = ftsRestClient.getDefaultResponsePageSize();
 190     Assert.assertEquals(defaultResSize, 100); // why 100 or 500 ? pdb is 100,
 191                                               // uniprot 500
 192   }
 193
 194   @Test(groups = { "Functional" })
 195   public void getColumnMinWidthTest()
 196   {
 197     try
 198     {
 199       FTSDataColumnI foundDataCol = ftsRestClient
 200               .getDataColumnByNameOrCode("uniprot_accession");
 201       Assert.assertNotNull(foundDataCol);
 202       int actualColMinWidth = foundDataCol.getMinWidth();
 203       Assert.assertEquals(actualColMinWidth, 50);
 204     } catch (Exception e)
 205     {
 206       e.printStackTrace();
 207       Assert.fail("Exception thrown while testing...");
 208     }
 209   }
 210   // could add test for MaxWidth & PreferedWith
 211
 212   @Test(groups = { "Functional" })
 213   public void getColumnClassTest()
 214   {
 215     try
 216     {
 217       FTSDataColumnI foundDataCol = ftsRestClient
 218               .getDataColumnByNameOrCode("uniprot_accession");
 219       Assert.assertNotNull(foundDataCol);
 220       Assert.assertEquals(foundDataCol.getDataType().getDataTypeClass(),
 221               String.class);
 222       foundDataCol = ftsRestClient.getDataColumnByNameOrCode("id");
 223       Assert.assertNotNull(foundDataCol);
 224       Assert.assertEquals(foundDataCol.getDataType().getDataTypeClass(),
 225               String.class);
 226     } catch (Exception e)
 227     {
 228       e.printStackTrace();
 229       Assert.fail("Exception thrown while testing...");
 230     }
 231   }
 232
 233   @Test(groups = { "Functional" })
 234   public void coverageForEqualsAndHashFunction()
 235   {
 236     Set<FTSDataColumnI> uniqueSet = new HashSet<FTSDataColumnI>();
 237     Collection<FTSDataColumnI> searchableCols = ftsRestClient
 238             .getSearchableDataColumns();
 239     System.out.println(searchableCols);
 240     for (FTSDataColumnI foundCol : searchableCols)
 241     {
 242       System.out.println(foundCol.toString());
 243       uniqueSet.add(foundCol);
 244       uniqueSet.add(foundCol);
 245     }
 246     Assert.assertTrue(!uniqueSet.isEmpty());
 247     // Assert.assertEquals(uniqueSet.size(), 22); -> 1 or 2 currently for 3DB
 248   }
 249
 250   @Test(groups = { "Functional" })
 251   public void getTDBIdColumIndexTest()
 252   {
 253     List<FTSDataColumnI> wantedFields = new ArrayList<FTSDataColumnI>();
 254     try
 255     {
 256       wantedFields.add(TDBeaconsFTSRestClient.getInstance()
 257               .getDataColumnByNameOrCode("Model id"));
 258       wantedFields.add(TDBeaconsFTSRestClient.getInstance()
 259               .getDataColumnByNameOrCode("uniprot_accession"));
 260       wantedFields.add(TDBeaconsFTSRestClient.getInstance()
 261               .getDataColumnByNameOrCode("entry name"));
 262     } catch (Exception e)
 263     {
 264       e.printStackTrace();
 265     }
 266     try
 267     {
 268       assertEquals(4, TDBeaconsFTSRestClient.getInstance()
 269               .getPrimaryKeyColumIndex(wantedFields, true));
 270       // assertEquals(3, TDBeaconsFTSRestClient.getInstance()
 271       // .getPrimaryKeyColumIndex(wantedFields, true));
 272     } catch (Exception e)
 273     {
 274       e.printStackTrace();
 275     }
 276   }
 277
 278   private static String mockRequest = "P38398.json";
 279
 280   private static String mockResponse = "{\"uniprot_entry\":{\"sequence_length\":1863,\"ac\":\"P38398\",\"id\":\"BRCA1_HUMAN\"},\"structures\":[{\"model_identifier\":\"4igk\",\"model_category\":\"EXPERIMENTALLY DETERMINED\",\"provider\":\"PDBE\",\"created\":\"2012-12-17\",\"sequence_identity\":100.0,\"uniprot_start\":1646,\"uniprot_end\":1859,\"resolution\":1.75,\"coverage\":11.49,\"model_url\":\"https://www.ebi.ac.uk/pdbe/static/entry/4igk_updated.cif\",\"model_format\":\"MMCIF\"},{\"model_identifier\":\"1t15\",\"model_category\":\"EXPERIMENTALLY DETERMINED\",\"provider\":\"PDBE\",\"created\":\"2004-04-15\",\"sequence_identity\":100.0,\"uniprot_start\":1646,\"uniprot_end\":1859,\"resolution\":1.85,\"coverage\":11.49,\"model_url\":\"https://www.ebi.ac.uk/pdbe/static/entry/1t15_updated.cif\",\"model_format\":\"MMCIF\"},{\"model_identifier\":\"4ifi\",\"model_category\":\"EXPERIMENTALLY DETERMINED\",\"provider\":\"PDBE\",\"created\":\"2012-12-14\",\"sequence_identity\":100.0,\"uniprot_start\":1646,\"uniprot_end\":1859,\"resolution\":2.2,\"coverage\":11.49,\"model_url\":\"https://www.ebi.ac.uk/pdbe/static/entry/4ifi_updated.cif\",\"model_format\":\"MMCIF\"},{\"model_identifier\":\"1t29\",\"model_category\":\"EXPERIMENTALLY DETERMINED\",\"provider\":\"PDBE\",\"created\":\"2004-04-20\",\"sequence_identity\":100.0,\"uniprot_start\":1646,\"uniprot_end\":1859,\"resolution\":2.3,\"coverage\":11.49,\"model_url\":\"https://www.ebi.ac.uk/pdbe/static/entry/1t29_updated.cif\",\"model_format\":\"MMCIF\"},{\"model_identifier\":\"3pxb\",\"model_category\":\"EXPERIMENTALLY DETERMINED\",\"provider\":\"PDBE\",\"created\":\"2010-12-09\",\"sequence_identity\":100.0,\"uniprot_start\":1646,\"uniprot_end\":1859,\"resolution\":2.5,\"coverage\":11.49,\"model_url\":\"https://www.ebi.ac.uk/pdbe/static/entry/3pxb_updated.cif\",\"model_format\":\"MMCIF\"},{\"model_identifier\":\"4y2g\",\"model_category\":\"EXPERIMENTALLY DETERMINED\",\"provider\":\"PDBE\",\"created\":\"2015-02-09\",\"sequence_identity\":100.0,\"uniprot_start\":1646,\"uniprot_end\":1859,\"resolution\":2.5,\"coverage\":11.49,\"model_url\":\"https://www.ebi.ac.uk/pdbe/static/entry/4y2g_updated.cif\",\"model_format\":\"MMCIF\"},{\"model_identifier\":\"1y98\",\"model_category\":\"EXPERIMENTALLY DETERMINED\",\"provider\":\"PDBE\",\"created\":\"2004-12-14\",\"sequence_identity\":100.0,\"uniprot_start\":1646,\"uniprot_end\":1859,\"resolution\":2.5,\"coverage\":11.49,\"model_url\":\"https://www.ebi.ac.uk/pdbe/static/entry/1y98_updated.cif\",\"model_format\":\"MMCIF\"},{\"model_identifier\":\"1jnx\",\"model_category\":\"EXPERIMENTALLY DETERMINED\",\"provider\":\"PDBE\",\"created\":\"2001-07-26\",\"sequence_identity\":100.0,\"uniprot_start\":1646,\"uniprot_end\":1859,\"resolution\":2.5,\"coverage\":11.49,\"model_url\":\"https://www.ebi.ac.uk/pdbe/static/entry/1jnx_updated.cif\",\"model_format\":\"MMCIF\"},{\"model_identifier\":\"3pxa\",\"model_category\":\"EXPERIMENTALLY DETERMINED\",\"provider\":\"PDBE\",\"created\":\"2010-12-09\",\"sequence_identity\":100.0,\"uniprot_start\":1646,\"uniprot_end\":1859,\"resolution\":2.55,\"coverage\":11.49,\"model_url\":\"https://www.ebi.ac.uk/pdbe/static/entry/3pxa_updated.cif\",\"model_format\":\"MMCIF\"},{\"model_identifier\":\"3k0h\",\"model_category\":\"EXPERIMENTALLY DETERMINED\",\"provider\":\"PDBE\",\"created\":\"2009-09-24\",\"sequence_identity\":100.0,\"uniprot_start\":1646,\"uniprot_end\":1859,\"resolution\":2.7,\"coverage\":11.49,\"model_url\":\"https://www.ebi.ac.uk/pdbe/static/entry/3k0h_updated.cif\",\"model_format\":\"MMCIF\"},{\"model_identifier\":\"3k0k\",\"model_category\":\"EXPERIMENTALLY DETERMINED\",\"provider\":\"PDBE\",\"created\":\"2009-09-24\",\"sequence_identity\":100.0,\"uniprot_start\":1646,\"uniprot_end\":1859,\"resolution\":2.7,\"coverage\":11.49,\"model_url\":\"https://www.ebi.ac.uk/pdbe/static/entry/3k0k_updated.cif\",\"model_format\":\"MMCIF\"},{\"model_identifier\":\"1n5o\",\"model_category\":\"EXPERIMENTALLY DETERMINED\",\"provider\":\"PDBE\",\"created\":\"2002-11-06\",\"sequence_identity\":100.0,\"uniprot_start\":1646,\"uniprot_end\":1859,\"resolution\":2.8,\"coverage\":11.49,\"model_url\":\"https://www.ebi.ac.uk/pdbe/static/entry/1n5o_updated.cif\",\"model_format\":\"MMCIF\"},{\"model_identifier\":\"3pxc\",\"model_category\":\"EXPERIMENTALLY DETERMINED\",\"provider\":\"PDBE\",\"created\":\"2010-12-09\",\"sequence_identity\":100.0,\"uniprot_start\":1646,\"uniprot_end\":1859,\"resolution\":2.8,\"coverage\":11.49,\"model_url\":\"https://www.ebi.ac.uk/pdbe/static/entry/3pxc_updated.cif\",\"model_format\":\"MMCIF\"},{\"model_identifier\":\"3pxd\",\"model_category\":\"EXPERIMENTALLY DETERMINED\",\"provider\":\"PDBE\",\"created\":\"2010-12-09\",\"sequence_identity\":100.0,\"uniprot_start\":1646,\"uniprot_end\":1859,\"resolution\":2.8,\"coverage\":11.49,\"model_url\":\"https://www.ebi.ac.uk/pdbe/static/entry/3pxd_updated.cif\",\"model_format\":\"MMCIF\"},{\"model_identifier\":\"1t2u\",\"model_category\":\"EXPERIMENTALLY DETERMINED\",\"provider\":\"PDBE\",\"created\":\"2004-04-22\",\"sequence_identity\":100.0,\"uniprot_start\":1646,\"uniprot_end\":1859,\"resolution\":2.8,\"coverage\":11.49,\"model_url\":\"https://www.ebi.ac.uk/pdbe/static/entry/1t2u_updated.cif\",\"model_format\":\"MMCIF\"},{\"model_identifier\":\"3k15\",\"model_category\":\"EXPERIMENTALLY DETERMINED\",\"provider\":\"PDBE\",\"created\":\"2009-09-25\",\"sequence_identity\":100.0,\"uniprot_start\":1646,\"uniprot_end\":1859,\"resolution\":2.8,\"coverage\":11.49,\"model_url\":\"https://www.ebi.ac.uk/pdbe/static/entry/3k15_updated.cif\",\"model_format\":\"MMCIF\"},{\"model_identifier\":\"3pxe\",\"model_category\":\"EXPERIMENTALLY DETERMINED\",\"provider\":\"PDBE\",\"created\":\"2010-12-09\",\"sequence_identity\":100.0,\"uniprot_start\":1646,\"uniprot_end\":1859,\"resolution\":2.85,\"coverage\":11.49,\"model_url\":\"https://www.ebi.ac.uk/pdbe/static/entry/3pxe_updated.cif\",\"model_format\":\"MMCIF\"},{\"model_identifier\":\"3k16\",\"model_category\":\"EXPERIMENTALLY DETERMINED\",\"provider\":\"PDBE\",\"created\":\"2009-09-25\",\"sequence_identity\":100.0,\"uniprot_start\":1646,\"uniprot_end\":1859,\"resolution\":3.0,\"coverage\":11.49,\"model_url\":\"https://www.ebi.ac.uk/pdbe/static/entry/3k16_updated.cif\",\"model_format\":\"MMCIF\"},{\"model_identifier\":\"4ofb\",\"model_category\":\"EXPERIMENTALLY DETERMINED\",\"provider\":\"PDBE\",\"created\":\"2014-01-14\",\"sequence_identity\":100.0,\"uniprot_start\":1646,\"uniprot_end\":1859,\"resolution\":3.05,\"coverage\":11.49,\"model_url\":\"https://www.ebi.ac.uk/pdbe/static/entry/4ofb_updated.cif\",\"model_format\":\"MMCIF\"},{\"model_identifier\":\"3coj\",\"model_category\":\"EXPERIMENTALLY DETERMINED\",\"provider\":\"PDBE\",\"created\":\"2008-03-28\",\"sequence_identity\":100.0,\"uniprot_start\":1646,\"uniprot_end\":1859,\"resolution\":3.21,\"coverage\":11.49,\"model_url\":\"https://www.ebi.ac.uk/pdbe/static/entry/3coj_updated.cif\",\"model_format\":\"MMCIF\"},{\"model_identifier\":\"7lyb\",\"model_category\":\"EXPERIMENTALLY DETERMINED\",\"provider\":\"PDBE\",\"created\":\"2021-03-06\",\"sequence_identity\":100.0,\"uniprot_start\":1,\"uniprot_end\":100,\"resolution\":3.28,\"coverage\":5.37,\"model_url\":\"https://www.ebi.ac.uk/pdbe/static/entry/7lyb_updated.cif\",\"model_format\":\"MMCIF\"},{\"model_identifier\":\"1t2v\",\"model_category\":\"EXPERIMENTALLY DETERMINED\",\"provider\":\"PDBE\",\"created\":\"2004-04-22\",\"sequence_identity\":100.0,\"uniprot_start\":1646,\"uniprot_end\":1859,\"resolution\":3.3,\"coverage\":11.49,\"model_url\":\"https://www.ebi.ac.uk/pdbe/static/entry/1t2v_updated.cif\",\"model_format\":\"MMCIF\"},{\"model_identifier\":\"4y18\",\"model_category\":\"EXPERIMENTALLY DETERMINED\",\"provider\":\"PDBE\",\"created\":\"2015-02-06\",\"sequence_identity\":100.0,\"uniprot_start\":1646,\"uniprot_end\":1859,\"resolution\":3.5,\"coverage\":11.49,\"model_url\":\"https://www.ebi.ac.uk/pdbe/static/entry/4y18_updated.cif\",\"model_format\":\"MMCIF\"},{\"model_identifier\":\"4jlu\",\"model_category\":\"EXPERIMENTALLY DETERMINED\",\"provider\":\"PDBE\",\"created\":\"2013-03-13\",\"sequence_identity\":100.0,\"uniprot_start\":1649,\"uniprot_end\":1859,\"resolution\":3.5,\"coverage\":11.33,\"model_url\":\"https://www.ebi.ac.uk/pdbe/static/entry/4jlu_updated.cif\",\"model_format\":\"MMCIF\"},{\"model_identifier\":\"4u4a\",\"model_category\":\"EXPERIMENTALLY DETERMINED\",\"provider\":\"PDBE\",\"created\":\"2014-07-23\",\"sequence_identity\":100.0,\"uniprot_start\":1646,\"uniprot_end\":1859,\"resolution\":3.51,\"coverage\":11.49,\"model_url\":\"https://www.ebi.ac.uk/pdbe/static/entry/4u4a_updated.cif\",\"model_format\":\"MMCIF\"},{\"model_identifier\":\"2ing\",\"model_category\":\"EXPERIMENTALLY DETERMINED\",\"provider\":\"PDBE\",\"created\":\"2006-10-07\",\"sequence_identity\":100.0,\"uniprot_start\":1649,\"uniprot_end\":1859,\"resolution\":3.6,\"coverage\":11.33,\"model_url\":\"https://www.ebi.ac.uk/pdbe/static/entry/2ing_updated.cif\",\"model_format\":\"MMCIF\"},{\"model_identifier\":\"7jzv\",\"model_category\":\"EXPERIMENTALLY DETERMINED\",\"provider\":\"PDBE\",\"created\":\"2020-09-02\",\"sequence_identity\":99.0,\"uniprot_start\":2,\"uniprot_end\":104,\"resolution\":3.9,\"coverage\":5.53,\"model_url\":\"https://www.ebi.ac.uk/pdbe/static/entry/7jzv_updated.cif\",\"model_format\":\"MMCIF\"},{\"model_identifier\":\"6g2i\",\"model_category\":\"EXPERIMENTALLY DETERMINED\",\"provider\":\"PDBE\",\"created\":\"2018-03-23\",\"sequence_identity\":100.0,\"uniprot_start\":1646,\"uniprot_end\":1859,\"resolution\":5.9,\"coverage\":11.49,\"model_url\":\"https://www.ebi.ac.uk/pdbe/static/entry/6g2i_updated.cif\",\"model_format\":\"MMCIF\"},{\"model_identifier\":\"1jm7\",\"model_category\":\"EXPERIMENTALLY DETERMINED\",\"provider\":\"PDBE\",\"created\":\"2001-07-17\",\"sequence_identity\":100.0,\"uniprot_start\":1,\"uniprot_end\":110,\"resolution\":null,\"coverage\":5.9,\"model_url\":\"https://www.ebi.ac.uk/pdbe/static/entry/1jm7_updated.cif\",\"model_format\":\"MMCIF\"},{\"model_identifier\":\"1oqa\",\"model_category\":\"EXPERIMENTALLY DETERMINED\",\"provider\":\"PDBE\",\"created\":\"2003-03-07\",\"sequence_identity\":100.0,\"uniprot_start\":1755,\"uniprot_end\":1863,\"resolution\":null,\"coverage\":5.85,\"model_url\":\"https://www.ebi.ac.uk/pdbe/static/entry/1oqa_updated.cif\",\"model_format\":\"MMCIF\"},{\"model_identifier\":\"6138930b772bfbf9fe34f912\",\"model_category\":\"TEMPLATE-BASED\",\"provider\":\"SWISSMODEL\",\"created\":\"2021-09-08\",\"sequence_identity\":1.0,\"uniprot_start\":1646,\"uniprot_end\":1859,\"coverage\":0.115,\"qmean_version\":\"4.2.0\",\"qmean_avg_local_score\":0.776,\"model_url\":\"https://beta.swissmodel.expasy.org/3d-beacons/uniprot/P38398.pdb?range=1646-1859&template=6g2i.1.K&provider=swissmodel\",\"model_format\":\"PDB\"},{\"model_identifier\":\"6138930b772bfbf9fe34f916\",\"model_category\":\"TEMPLATE-BASED\",\"provider\":\"SWISSMODEL\",\"created\":\"2021-09-08\",\"sequence_identity\":1.0,\"uniprot_start\":1,\"uniprot_end\":103,\"coverage\":0.055,\"qmean_version\":\"4.2.0\",\"qmean_avg_local_score\":0.655,\"model_url\":\"https://beta.swissmodel.expasy.org/3d-beacons/uniprot/P38398.pdb?range=1-103&template=1jm7.1.A&provider=swissmodel\",\"model_format\":\"PDB\"},{\"model_identifier\":\"AF-P38398-F1\",\"model_category\":\"Deep learning\",\"provider\":\"AlphaFold DB\",\"created\":\"2021-07-01\",\"sequence_identity\":1.0,\"uniprot_start\":1,\"uniprot_end\":1863,\"coverage\":100.0,\"model_url\":\"https://alphafold.ebi.ac.uk/files/AF-P38398-F1-model_v1.cif\",\"model_format\":\"MMCIF\"}]}";
 281
 282   public static void setMock()
 283   {
 284     FTSRestClient.createMockFTSRestClient(
 285             (FTSRestClient) TDBeaconsFTSRestClient.getInstance(),
 286             mockRequest, mockResponse);
 287   }
 288
 289   private static String dev_url = "https://wwwdev.ebi.ac.uk/pdbe/pdbe-kb/3dbeacons/api/uniprot/summary/";
 290
 291   /**
 292    * check that the mock request and response are the same as the response from
 293    * a live 3D-beacons endpoint
 294    *
 295    * @throws Exception
 296    */
 297   @Test(groups = { "Network", "Integration" })
 298   public void verifyMockTDBRequest() throws Exception
 299   {
 300     URL tdb_req = new URL(dev_url + mockRequest);
 301     byte[] resp = tdb_req.openStream().readAllBytes();
 302     String tresp = new String(resp, StandardCharsets.UTF_8);
 303     assertEquals(mockResponse.trim(), tresp.trim());
 304   }
 305
 306   @Test(groups = { "Functional" })
 307   public void testMockTDBRequest()
 308   {
 309
 310     setMock();
 311     List<FTSDataColumnI> wantedFields = new ArrayList<FTSDataColumnI>();
 312     try
 313     {
 314       wantedFields.add(TDBeaconsFTSRestClient.getInstance()
 315               .getDataColumnByNameOrCode("Model Id"));
 316       wantedFields.add(TDBeaconsFTSRestClient.getInstance()
 317               .getDataColumnByNameOrCode("model_url"));
 318       wantedFields.add(TDBeaconsFTSRestClient.getInstance()
 319               .getDataColumnByNameOrCode("provider"));
 320       wantedFields.add(TDBeaconsFTSRestClient.getInstance()
 321               .getDataColumnByNameOrCode("model_category"));
 322       wantedFields.add(TDBeaconsFTSRestClient.getInstance()
 323               .getDataColumnByNameOrCode("qmean_avg_local_score"));
 324       wantedFields.add(TDBeaconsFTSRestClient.getInstance()
 325               .getDataColumnByNameOrCode("uniprot_start"));
 326       wantedFields.add(TDBeaconsFTSRestClient.getInstance()
 327               .getDataColumnByNameOrCode("uniprot_end"));
 328     } catch (Exception e1)
 329     {
 330       e1.printStackTrace();
 331     }
 332     System.out.println("wantedFields >>" + wantedFields);
 333
 334     FTSRestRequest request = new FTSRestRequest();
 335     FTSRestResponse response;
 336
 337     request.setResponseSize(100);
 338     request.setFieldToSearchBy("");
 339     request.setWantedFields(wantedFields);
 340     // check 404 behaviour
 341     request.setSearchTerm("P00000.json");
 342
 343     try
 344     {
 345       response = TDBeaconsFTSRestClient.getInstance()
 346               .executeRequest(request);
 347
 348       assertNull(response);
 349     } catch (Exception e)
 350     {
 351       e.printStackTrace();
 352       Assert.fail("Unexpected failure during mock 3DBeacons 404 test");
 353     }
 354
 355     // check 200 behaviour
 356     request.setSearchTerm("P38398.json");
 357     System.out.println("request : " + request.getFieldToSearchBy());
 358     // System.out.println(request.toString());
 359
 360     try
 361     {
 362       response = TDBeaconsFTSRestClient.getInstance()
 363               .executeRequest(request);
 364     } catch (Exception e)
 365     {
 366       e.printStackTrace();
 367       Assert.fail("Couldn't execute webservice call!");
 368       return;
 369     }
 370     assertTrue(response.getSearchSummary() != null);
 371     assertTrue(response.getNumberOfItemsFound() > 3); // 4 atm
 372     System.out.println("Search summary : \n" + response.getSearchSummary());
 373
 374     // System.out.println(response.getSearchSummary().size());
 375   }
 376
 377   @Test(groups = { "External", "Network" })
 378   public void executeRequestTest()
 379   {
 380     List<FTSDataColumnI> wantedFields = new ArrayList<FTSDataColumnI>();
 381     try
 382     {
 383       wantedFields.add(TDBeaconsFTSRestClient.getInstance()
 384               .getDataColumnByNameOrCode("Model Id"));
 385       wantedFields.add(TDBeaconsFTSRestClient.getInstance()
 386               .getDataColumnByNameOrCode("model_url"));
 387       wantedFields.add(TDBeaconsFTSRestClient.getInstance()
 388               .getDataColumnByNameOrCode("provider"));
 389       wantedFields.add(TDBeaconsFTSRestClient.getInstance()
 390               .getDataColumnByNameOrCode("model_category"));
 391       wantedFields.add(TDBeaconsFTSRestClient.getInstance()
 392               .getDataColumnByNameOrCode("qmean_avg_local_score"));
 393       wantedFields.add(TDBeaconsFTSRestClient.getInstance()
 394               .getDataColumnByNameOrCode("uniprot_start"));
 395       wantedFields.add(TDBeaconsFTSRestClient.getInstance()
 396               .getDataColumnByNameOrCode("uniprot_end"));
 397     } catch (Exception e1)
 398     {
 399       e1.printStackTrace();
 400     }
 401     System.out.println("wantedFields >>" + wantedFields);
 402
 403     FTSRestRequest request = new FTSRestRequest();
 404     request.setResponseSize(100);
 405     request.setFieldToSearchBy("");
 406     request.setSearchTerm("P01318.json");
 407     request.setWantedFields(wantedFields);
 408     System.out.println("request : " + request.getFieldToSearchBy());
 409     // System.out.println(request.toString());
 410
 411     FTSRestResponse response;
 412     try
 413     {
 414       response = TDBeaconsFTSRestClient.getInstance()
 415               .executeRequest(request);
 416     } catch (Exception e)
 417     {
 418       e.printStackTrace();
 419       Assert.fail("Couldn't execute webservice call!");
 420       return;
 421     }
 422     assertTrue(response.getSearchSummary() != null);
 423     assertTrue(response.getNumberOfItemsFound() > 3); // 4 atm
 424     System.out.println("Search summary : \n" + response.getSearchSummary());
 425     // System.out.println(response.getSearchSummary().size());
 426   }
 427 }